{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T16:48:14Z","timestamp":1780764494950,"version":"3.54.1"},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,6,20]],"date-time":"2020-06-20T00:00:00Z","timestamp":1592611200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2020,6,20]],"date-time":"2020-06-20T00:00:00Z","timestamp":1592611200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"funder":[{"DOI":"10.13039\/501100002790","name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2019-04696"],"award-info":[{"award-number":["RGPIN-2019-04696"]}],"id":[{"id":"10.13039\/501100002790","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002790","name":"Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2016-05017"],"award-info":[{"award-number":["RGPIN-2016-05017"]}],"id":[{"id":"10.13039\/501100002790","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Netw Model Anal Health Inform Bioinforma"],"published-print":{"date-parts":[[2020,12]]},"DOI":"10.1007\/s13721-020-00249-4","type":"journal-article","created":{"date-parts":[[2020,6,20]],"date-time":"2020-06-20T21:02:17Z","timestamp":1592686937000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["A novel approach to identify subtype-specific network biomarkers of breast cancer survivability"],"prefix":"10.1007","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0416-7866","authenticated-orcid":false,"given":"Sheikh","family":"Jubair","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1751-7570","authenticated-orcid":false,"given":"Abedalrhman","family":"Alkhateeb","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4845-0767","authenticated-orcid":false,"given":"Ashraf Abou","family":"Tabl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7988-2058","authenticated-orcid":false,"given":"Luis","family":"Rueda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2092-2494","authenticated-orcid":false,"given":"Alioune","family":"Ngom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,6,20]]},"reference":[{"key":"249_CR1","doi-asserted-by":"publisher","first-page":"256","DOI":"10.3389\/fgene.2019.00256","volume":"10","author":"A Abou Tabl","year":"2019","unstructured":"Abou Tabl A, Alkhateeb A, ElMaraghy W, Rueda L, Ngom A (2019) A machine learning approach for identifying gene biomarkers guiding the treatment of breast cancer. Front Genet 10:256","journal-title":"Front Genet"},{"issue":"12","key":"249_CR2","doi-asserted-by":"publisher","first-page":"i311","DOI":"10.1093\/bioinformatics\/btv255","volume":"31","author":"A Allahyar","year":"2015","unstructured":"Allahyar A, de Ridder J (2015) Feral: network-based classifier with application to breast cancer outcome prediction. Bioinformatics 31(12):i311\u2013i319","journal-title":"Bioinformatics"},{"issue":"1","key":"249_CR3","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman L (2001) Random forests. Mach Learn 45(1):5\u201332","journal-title":"Mach Learn"},{"issue":"8","key":"249_CR4","doi-asserted-by":"publisher","first-page":"2329","DOI":"10.1158\/1078-0432.CCR-06-1109","volume":"13","author":"LA Carey","year":"2007","unstructured":"Carey LA, Claire Dees E, Sawyer L, Gatti L, Moore DT, Collichio F, Ollila DW, Sartor CI, Graham ML, Perou CM (2007) The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res 13(8):2329\u20132334","journal-title":"Clin Cancer Res"},{"key":"249_CR5","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1613\/jair.953","volume":"16","author":"NV Chawla","year":"2002","unstructured":"Chawla NV, Bowyer KW, Hall LO, Philip Kegelmeyer W (2002) Smote: synthetic minority over-sampling technique. J Artif Intell Res 16:321\u2013357","journal-title":"J Artif Intell Res"},{"issue":"1","key":"249_CR6","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1038\/msb4100180","volume":"3","author":"H-Y Chuang","year":"2007","unstructured":"Chuang H-Y, Lee E, Liu Y-T, Lee D, Ideker T (2007) Network-based classification of breast cancer metastasis. Mol Syst Biol 3(1):140","journal-title":"Mol Syst Biol"},{"issue":"7403","key":"249_CR7","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1038\/nature10983","volume":"486","author":"C Curtis","year":"2012","unstructured":"Curtis C, Shah SP, Chin S-F, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y et al (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486(7403):346\u2013352","journal-title":"Nature"},{"issue":"13","key":"249_CR8","doi-asserted-by":"publisher","first-page":"i205","DOI":"10.1093\/bioinformatics\/btr245","volume":"27","author":"P Dao","year":"2011","unstructured":"Dao P, Wang K, Collins C, Ester M, Lapuk A, Cenk Sahinalp S (2011) Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics 27(13):i205\u2013i213","journal-title":"Bioinformatics"},{"issue":"5","key":"249_CR9","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/emboj.2013.19","volume":"32","author":"S-J Dawson","year":"2013","unstructured":"Dawson S-J, Rueda OM, Aparicio S, Caldas C (2013) A new genome-driven integrated classification of breast cancer and its implications. EMBO J 32(5):617\u2013628","journal-title":"EMBO J"},{"issue":"1","key":"249_CR10","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1471-2105-13-71","volume":"13","author":"W Duojiao","year":"2012","unstructured":"Duojiao W, Rice CM, Wang X (2012) Cancer bioinformatics: a new approach to systems clinical medicine. BMC Bioinf 13(1):71","journal-title":"BMC Bioinf"},{"issue":"1","key":"249_CR11","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/s12859-017-1559-2","volume":"18","author":"A Fabregat","year":"2017","unstructured":"Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D\u2019Eustachio P, Stein L, Hermjakob H (2017) Reactome pathway analysis: a high-performance in-memory approach. BMC Bioinf 18(1):142","journal-title":"BMC Bioinf"},{"issue":"2","key":"249_CR12","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1016\/0046-8177(95)90039-X","volume":"26","author":"W Fraser Symmans","year":"1995","unstructured":"Fraser Symmans W, Liu J, Knowles DM, Inghirami G (1995) Breast cancer heterogeneity: evaluation of clonality in primary and metastatic lesions. Hum Pathol 26(2):210\u2013216","journal-title":"Hum Pathol"},{"issue":"1","key":"249_CR13","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1186\/s12859-015-0551-y","volume":"16","author":"K Glass","year":"2015","unstructured":"Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan G-C (2015) A network model for angiogenesis in ovarian cancer. BMC Bioinf 16(1):115","journal-title":"BMC Bioinf"},{"issue":"7132","key":"249_CR14","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/nature05610","volume":"446","author":"C Greenman","year":"2007","unstructured":"Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C et al (2007) Patterns of somatic mutation in human cancer genomes. Nature 446(7132):153\u2013158","journal-title":"Nature"},{"key":"249_CR15","unstructured":"Hahn Milton E, MacLean Malcolm S (1955) Prognosis and prediction"},{"issue":"5","key":"249_CR16","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646\u2013674","journal-title":"Cell"},{"key":"249_CR17","unstructured":"He H, Bai Y, Garcia EA, Li S (2008) Adasyn: Adaptive synthetic sampling approach for imbalanced learning. In: Neural Networks, 2008. IJCNN 2008. (IEEE World Congress on Computational Intelligence). IEEE International Joint Conference on, pp 1322\u20131328. IEEE"},{"key":"249_CR18","doi-asserted-by":"crossref","unstructured":"Khoshgoftaar TM, Seiffert C, Van Hulse J, Napolitano A, Folleco A (2007) Learning with limited minority class data. In: Machine learning and applications, ICMLA 2","DOI":"10.1109\/ICMLA.2007.76"},{"issue":"D1","key":"249_CR19","doi-asserted-by":"publisher","first-page":"D1071","DOI":"10.1093\/nar\/gku1011","volume":"43","author":"WA Kibbe","year":"2015","unstructured":"Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D et al (2015) Disease ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res 43(D1):D1071\u2013D1078","journal-title":"Nucleic Acids Res"},{"issue":"52","key":"249_CR20","doi-asserted-by":"publisher","first-page":"20793","DOI":"10.1073\/pnas.0710343105","volume":"104","author":"JH Kim","year":"2007","unstructured":"Kim JH, Lee JM, Nam HJ, Choi HJ, Yang JW, Lee JS, Kim MH, Kim S-I, Chung CH, Kim KI et al (2007) Sumoylation of pontin chromatin-remodeling complex reveals a signal integration code in prostate cancer cells. Proc Nat Acad Sci 104(52):20793\u201320798","journal-title":"Proc Nat Acad Sci"},{"issue":"2","key":"249_CR21","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1586\/erp.13.4","volume":"13","author":"NWD Lamond","year":"2013","unstructured":"Lamond NWD, Skedgel C, Younis T (2013) Is the 21-gene recurrence score a cost-effective assay in endocrine-sensitive node-negative breast cancer? Expert Rev Pharmacoecon Outcomes Res 13(2):243\u2013250","journal-title":"Expert Rev Pharmacoecon Outcomes Res"},{"issue":"11","key":"249_CR22","doi-asserted-by":"publisher","first-page":"e1000217","DOI":"10.1371\/journal.pcbi.1000217","volume":"4","author":"E Lee","year":"2008","unstructured":"Lee E, Chuang H-Y, Kim J-W, Ideker T, Lee D (2008) Inferring pathway activity toward precise disease classification. PLoS Comput Biol 4(11):e1000217","journal-title":"PLoS Comput Biol"},{"issue":"7","key":"249_CR23","doi-asserted-by":"publisher","first-page":"e0129711","DOI":"10.1371\/journal.pone.0129711","volume":"10","author":"HH Milioli","year":"2015","unstructured":"Milioli HH, Vimieiro R, Riveros C, Tishchenko I, Berretta R, Moscato P (2015) The discovery of novel biomarkers improves breast cancer intrinsic subtype prediction and reconciles the labels in the metabric data set. PLoS One 10(7):e0129711","journal-title":"PLoS One"},{"key":"249_CR24","doi-asserted-by":"crossref","unstructured":"Mucaki EJ, Baranova K, Pham HQ, Rezaeian I, Angelov D, Ngom A, Rueda L, Rogan PK (2016) Predicting outcomes of hormone and chemotherapy in the molecular taxonomy of breast cancer international consortium (metabric) study by biochemically-inspired machine learning. F1000Research, vol. 5","DOI":"10.12688\/f1000research.9417.3"},{"issue":"7418","key":"249_CR25","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/nature11412","volume":"490","author":"CGA Network","year":"2012","unstructured":"Network CGA et al (2012) Comprehensive molecular portraits of human breast tumors. Nature 490(7418):61","journal-title":"Nature"},{"issue":"16","key":"249_CR26","doi-asserted-by":"publisher","first-page":"5678","DOI":"10.1158\/1078-0432.CCR-04-2421","volume":"11","author":"R Rouzier","year":"2005","unstructured":"Rouzier R, Perou CM, Fraser Symmans W, Ibrahim N, Cristofanilli M, Anderson K, Hess KR, Stec J, Ayers M, Wagner P et al (2005) Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 11(16):5678\u20135685","journal-title":"Clin Cancer Res"},{"issue":"7187","key":"249_CR27","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1038\/nature06913","volume":"452","author":"CL Sawyers","year":"2008","unstructured":"Sawyers CL (2008) The cancer biomarker problem. Nature 452(7187):548\u2013552","journal-title":"Nature"},{"issue":"8","key":"249_CR28","doi-asserted-by":"publisher","first-page":"829","DOI":"10.2217\/pme.12.87","volume":"9","author":"JE Schneider","year":"2012","unstructured":"Schneider JE, Sidhu MK, Doucet C, Kiss N, Ohsfeldt RL, Chalfin D (2012) Economics of cancer biomarkers. Person Med 9(8):829\u2013837","journal-title":"Person Med"},{"key":"249_CR29","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.genrep.2015.12.001","volume":"3","author":"JDJ Sheeba","year":"2016","unstructured":"Sheeba JDJ, Mohan C, Marine H, Gauri D, Neeraj K, Mukund LA (2016) Estrogen-regulated extracellular matrix remodeling genes in mcf-7 breast cancer cells. Gene Rep 3:14\u201321","journal-title":"Gene Rep"},{"issue":"6","key":"249_CR30","doi-asserted-by":"publisher","first-page":"e100335","DOI":"10.1371\/journal.pone.0100335","volume":"9","author":"C Soneson","year":"2014","unstructured":"Soneson C, Gerster S, Delorenzi M (2014) Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation. PLoS One 9(6):e100335","journal-title":"PLoS One"},{"key":"249_CR31","doi-asserted-by":"crossref","unstructured":"Tabl Ashraf Abou, Alkhateeb Abedalrhman, Rueda Luis, ElMaraghy Waguih, Ngom Alioune (2018) Identification of the treatment survivability gene biomarkers of breast cancer patients via a tree-based approach. In: International conference on bioinformatics and biomedical engineering. Springer, Berlin, pp 166\u2013176","DOI":"10.1007\/978-3-319-78723-7_14"},{"issue":"26","key":"249_CR32","doi-asserted-by":"publisher","first-page":"4270","DOI":"10.1200\/JCO.2006.05.9493","volume":"24","author":"N Umetani","year":"2006","unstructured":"Umetani N, Giuliano AE, Hiramatsu SH, Amersi F, Nakagawa T, Martino S, Hoon DSB (2006) Prediction of breast tumor progression by integrity of free circulating dna in serum. J Clin Oncol 24(26):4270\u20134276","journal-title":"J Clin Oncol"},{"issue":"2","key":"249_CR33","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1515\/jib-2011-188","volume":"8","author":"E van den Akker","year":"2011","unstructured":"van den Akker E, Verbruggen B, Heijmans B, Beekman M, Kok J, Slagboom E, Reinders M (2011) Integrating protein-protein interaction networks with gene-gene co-expression networks improves gene signatures for classifying breast cancer metastasis. J Integr Bioinf (JIB) 8(2):222\u2013238","journal-title":"J Integr Bioinf (JIB)"},{"issue":"1","key":"249_CR34","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.critrevonc.2006.04.002","volume":"60","author":"M Verma","year":"2006","unstructured":"Verma M, Manne U (2006) Genetic and epigenetic biomarkers in cancer diagnosis and identifying high risk populations. Crit Rev Oncol Hematol 60(1):9\u201318","journal-title":"Crit Rev Oncol Hematol"},{"issue":"6127","key":"249_CR35","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1126\/science.1235122","volume":"339","author":"B Vogelstein","year":"2013","unstructured":"Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW (2013) Cancer genome landscapes. Science 339(6127):1546\u20131558","journal-title":"Science"},{"issue":"4","key":"249_CR36","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1159\/000151225","volume":"54","author":"W-J Wang","year":"2008","unstructured":"Wang W-J, Li Q-Q, Xu J-D, Cao X-X, Li H-X, Tang F, Chen Q, Yang J-M, Xu Z-D, Liu X-P (2008) Interaction between cd147 and p-glycoprotein and their regulation by ubiquitination in breast cancer cells. Chemotherapy 54(4):291\u2013301","journal-title":"Chemotherapy"},{"issue":"5853","key":"249_CR37","doi-asserted-by":"publisher","first-page":"1108","DOI":"10.1126\/science.1145720","volume":"318","author":"LD Wood","year":"2007","unstructured":"Wood LD, Williams Parsons D, Jones S, Lin J, Sj\u00f6blom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J et al (2007) The genomic landscapes of human breast and colorectal cancers. Science 318(5853):1108\u20131113","journal-title":"Science"},{"issue":"S5","key":"249_CR38","doi-asserted-by":"publisher","first-page":"S4","DOI":"10.1186\/1471-2164-14-S5-S4","volume":"14","author":"Y Xiang","year":"2013","unstructured":"Xiang Y, Zhang J, Huang K (2013) Mining the tissue-tissue gene co-expression network for tumor microenvironment study and biomarker prediction. BMC Genom 14(S5):S4","journal-title":"BMC Genom"},{"issue":"22","key":"249_CR39","doi-asserted-by":"crossref","first-page":"11619","DOI":"10.1074\/jbc.M115.713370","volume":"291","author":"D Yamashita","year":"2016","unstructured":"Yamashita D, Moriuchi T, Osumi T, Hirose F (2016) Transcription factor hdref is a novel sumo e3 ligase of mi2$$\\alpha$$. J Biol Chem 291(22):11619\u201311634","journal-title":"J Biol Chem"}],"container-title":["Network Modeling Analysis in Health Informatics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-020-00249-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s13721-020-00249-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s13721-020-00249-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,6,19]],"date-time":"2021-06-19T23:44:28Z","timestamp":1624146268000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s13721-020-00249-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,20]]},"references-count":39,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["249"],"URL":"https:\/\/doi.org\/10.1007\/s13721-020-00249-4","relation":{},"ISSN":["2192-6662","2192-6670"],"issn-type":[{"value":"2192-6662","type":"print"},{"value":"2192-6670","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,20]]},"assertion":[{"value":"29 January 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 May 2020","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2020","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 June 2020","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with ethical standards"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}},{"value":"The datasets analysed during the current study are available in the cBioPortal repository at . The resulting PPI network is included in the following link: <i>Supplementary materials<\/i>: . .","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Availability of data and material"}}],"article-number":"43"}}